Calcium in PDB 3qrb: Crystal Structure of E-Cadherin EC1-2 P5A P6A
Protein crystallography data
The structure of Crystal Structure of E-Cadherin EC1-2 P5A P6A, PDB code: 3qrb
was solved by
X.Jin,
L.Shapiro,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
44.70 /
1.80
|
|
Space group
|
C 1 2 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
111.185,
92.583,
79.465,
90.00,
92.26,
90.00
|
|
R / Rfree (%)
|
16.2 /
17.8
|
Calcium Binding Sites:
The binding sites of Calcium atom in the Crystal Structure of E-Cadherin EC1-2 P5A P6A
(pdb code 3qrb). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the
Crystal Structure of E-Cadherin EC1-2 P5A P6A, PDB code: 3qrb:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
6;
Calcium binding site 1 out
of 6 in 3qrb
Go back to
Calcium Binding Sites List in 3qrb
Calcium binding site 1 out
of 6 in the Crystal Structure of E-Cadherin EC1-2 P5A P6A
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of Crystal Structure of E-Cadherin EC1-2 P5A P6A within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca301
b:13.5
occ:1.00
|
OE1
|
A:GLU69
|
2.2
|
19.6
|
1.0
|
|
OD1
|
A:ASP67
|
2.3
|
17.6
|
1.0
|
|
OD2
|
A:ASP103
|
2.3
|
19.2
|
1.0
|
|
OE1
|
A:GLU11
|
2.4
|
17.7
|
1.0
|
|
O
|
A:HOH287
|
2.4
|
7.2
|
1.0
|
|
O
|
A:HOH288
|
2.4
|
7.3
|
1.0
|
|
CG
|
A:ASP103
|
3.1
|
18.9
|
1.0
|
|
OD1
|
A:ASP103
|
3.2
|
16.9
|
1.0
|
|
CG
|
A:ASP67
|
3.3
|
17.7
|
1.0
|
|
CD
|
A:GLU11
|
3.3
|
17.9
|
1.0
|
|
CD
|
A:GLU69
|
3.5
|
18.6
|
1.0
|
|
OE2
|
A:GLU11
|
3.7
|
18.9
|
1.0
|
|
OD2
|
A:ASP67
|
4.0
|
17.5
|
1.0
|
|
CA
|
A:CA302
|
4.0
|
13.6
|
1.0
|
|
N
|
A:ARG68
|
4.1
|
15.2
|
1.0
|
|
CA
|
A:ASP67
|
4.1
|
15.2
|
1.0
|
|
O
|
A:HOH408
|
4.2
|
15.2
|
1.0
|
|
CB
|
A:ASP67
|
4.2
|
16.2
|
1.0
|
|
N
|
A:GLU69
|
4.2
|
16.9
|
1.0
|
|
CB
|
A:GLU69
|
4.3
|
19.1
|
1.0
|
|
ND2
|
A:ASN104
|
4.3
|
15.6
|
1.0
|
|
CG
|
A:GLU69
|
4.4
|
19.6
|
1.0
|
|
OE2
|
A:GLU69
|
4.4
|
19.9
|
1.0
|
|
C
|
A:ASP67
|
4.4
|
15.9
|
1.0
|
|
OD1
|
A:ASN12
|
4.4
|
18.4
|
1.0
|
|
ND2
|
A:ASN12
|
4.4
|
20.1
|
1.0
|
|
O
|
A:HOH215
|
4.6
|
18.8
|
1.0
|
|
O
|
A:HOH239
|
4.6
|
19.8
|
1.0
|
|
CB
|
A:ASP103
|
4.6
|
18.6
|
1.0
|
|
CG
|
A:GLU11
|
4.6
|
17.6
|
1.0
|
|
O
|
A:HOH602
|
4.6
|
20.9
|
1.0
|
|
CG
|
A:ASN12
|
4.8
|
21.4
|
1.0
|
|
CA
|
A:GLU69
|
4.8
|
17.9
|
1.0
|
|
CB
|
A:GLU11
|
4.9
|
16.0
|
1.0
|
|
Calcium binding site 2 out
of 6 in 3qrb
Go back to
Calcium Binding Sites List in 3qrb
Calcium binding site 2 out
of 6 in the Crystal Structure of E-Cadherin EC1-2 P5A P6A
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of Crystal Structure of E-Cadherin EC1-2 P5A P6A within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca302
b:13.6
occ:1.00
|
OD1
|
A:ASP100
|
2.2
|
18.1
|
1.0
|
|
OE2
|
A:GLU11
|
2.3
|
18.9
|
1.0
|
|
OD1
|
A:ASP136
|
2.3
|
16.2
|
1.0
|
|
OD1
|
A:ASP103
|
2.3
|
16.9
|
1.0
|
|
OE2
|
A:GLU69
|
2.4
|
19.9
|
1.0
|
|
O
|
A:GLN101
|
2.4
|
18.4
|
1.0
|
|
OE1
|
A:GLU69
|
2.7
|
19.6
|
1.0
|
|
CD
|
A:GLU69
|
2.9
|
18.6
|
1.0
|
|
CG
|
A:ASP100
|
3.3
|
18.1
|
1.0
|
|
CG
|
A:ASP136
|
3.4
|
18.8
|
1.0
|
|
CD
|
A:GLU11
|
3.4
|
17.9
|
1.0
|
|
CG
|
A:ASP103
|
3.5
|
18.9
|
1.0
|
|
C
|
A:GLN101
|
3.6
|
19.2
|
1.0
|
|
OE1
|
A:GLU11
|
3.8
|
17.7
|
1.0
|
|
N
|
A:GLN101
|
3.8
|
19.0
|
1.0
|
|
OD2
|
A:ASP100
|
3.8
|
18.0
|
1.0
|
|
ND2
|
A:ASN104
|
3.9
|
15.6
|
1.0
|
|
CA
|
A:CA301
|
4.0
|
13.5
|
1.0
|
|
CB
|
A:ASP136
|
4.0
|
17.7
|
1.0
|
|
OD2
|
A:ASP103
|
4.0
|
19.2
|
1.0
|
|
N
|
A:ASP103
|
4.1
|
19.1
|
1.0
|
|
CA
|
A:ASP136
|
4.3
|
19.0
|
1.0
|
|
CG
|
A:GLU69
|
4.3
|
19.6
|
1.0
|
|
OD2
|
A:ASP136
|
4.3
|
13.9
|
1.0
|
|
CA
|
A:GLN101
|
4.3
|
20.0
|
1.0
|
|
NE
|
A:ARG68
|
4.4
|
20.4
|
1.0
|
|
CB
|
A:ASP100
|
4.5
|
18.6
|
1.0
|
|
CA
|
A:ASP100
|
4.6
|
18.8
|
1.0
|
|
CB
|
A:ASP103
|
4.6
|
18.6
|
1.0
|
|
N
|
A:ASN102
|
4.7
|
19.3
|
1.0
|
|
C
|
A:ASP100
|
4.7
|
19.4
|
1.0
|
|
CG
|
A:GLU11
|
4.7
|
17.6
|
1.0
|
|
CA
|
A:ASP103
|
4.8
|
19.1
|
1.0
|
|
CA
|
A:ASN102
|
4.8
|
19.3
|
1.0
|
|
NH2
|
A:ARG68
|
4.8
|
21.7
|
1.0
|
|
CB
|
A:ARG68
|
4.9
|
16.7
|
1.0
|
|
C
|
A:ASN102
|
5.0
|
19.9
|
1.0
|
|
CB
|
A:GLN101
|
5.0
|
20.5
|
1.0
|
|
Calcium binding site 3 out
of 6 in 3qrb
Go back to
Calcium Binding Sites List in 3qrb
Calcium binding site 3 out
of 6 in the Crystal Structure of E-Cadherin EC1-2 P5A P6A
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of Crystal Structure of E-Cadherin EC1-2 P5A P6A within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca303
b:16.4
occ:1.00
|
O
|
A:ASN104
|
2.3
|
19.7
|
1.0
|
|
OD2
|
A:ASP136
|
2.3
|
13.9
|
1.0
|
|
O
|
A:ASN143
|
2.3
|
19.4
|
1.0
|
|
OD1
|
A:ASN102
|
2.3
|
21.2
|
1.0
|
|
OD2
|
A:ASP195
|
2.3
|
20.6
|
1.0
|
|
OD2
|
A:ASP134
|
2.4
|
21.7
|
1.0
|
|
OD1
|
A:ASP134
|
2.6
|
20.2
|
1.0
|
|
CG
|
A:ASP134
|
2.8
|
22.3
|
1.0
|
|
CG
|
A:ASP195
|
3.4
|
21.4
|
1.0
|
|
CG
|
A:ASP136
|
3.4
|
18.8
|
1.0
|
|
C
|
A:ASN104
|
3.5
|
19.9
|
1.0
|
|
CG
|
A:ASN102
|
3.5
|
19.6
|
1.0
|
|
C
|
A:ASN143
|
3.5
|
18.8
|
1.0
|
|
CB
|
A:ASP136
|
3.8
|
17.7
|
1.0
|
|
CB
|
A:ASP195
|
3.8
|
20.3
|
1.0
|
|
ND2
|
A:ASN102
|
4.1
|
22.2
|
1.0
|
|
N
|
A:ASN104
|
4.2
|
18.5
|
1.0
|
|
CA
|
A:ASN104
|
4.3
|
19.3
|
1.0
|
|
CB
|
A:ASP134
|
4.4
|
18.9
|
1.0
|
|
OD1
|
A:ASP195
|
4.4
|
21.4
|
1.0
|
|
CA
|
A:ASN143
|
4.4
|
20.2
|
1.0
|
|
CB
|
A:ASN104
|
4.5
|
18.7
|
1.0
|
|
CB
|
A:ASN143
|
4.5
|
18.7
|
1.0
|
|
N
|
A:ALA144
|
4.5
|
19.2
|
1.0
|
|
OD1
|
A:ASP136
|
4.5
|
16.2
|
1.0
|
|
N
|
A:ARG105
|
4.6
|
21.3
|
1.0
|
|
CA
|
A:ALA144
|
4.6
|
19.9
|
1.0
|
|
CD1
|
A:LEU201
|
4.7
|
20.9
|
1.0
|
|
CD
|
A:PRO106
|
4.7
|
21.2
|
1.0
|
|
CB
|
A:ASN102
|
4.7
|
19.9
|
1.0
|
|
CA
|
A:ARG105
|
4.8
|
22.6
|
1.0
|
|
N
|
A:ASP136
|
4.8
|
17.6
|
1.0
|
|
CA
|
A:ASN102
|
4.8
|
19.3
|
1.0
|
|
C
|
A:ARG105
|
4.9
|
22.0
|
1.0
|
|
N
|
A:PRO106
|
4.9
|
21.9
|
1.0
|
|
CA
|
A:ASP136
|
4.9
|
19.0
|
1.0
|
|
C
|
A:ASN102
|
5.0
|
19.9
|
1.0
|
|
Calcium binding site 4 out
of 6 in 3qrb
Go back to
Calcium Binding Sites List in 3qrb
Calcium binding site 4 out
of 6 in the Crystal Structure of E-Cadherin EC1-2 P5A P6A
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of Crystal Structure of E-Cadherin EC1-2 P5A P6A within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca301
b:12.3
occ:1.00
|
OE1
|
B:GLU69
|
2.2
|
17.7
|
1.0
|
|
OD1
|
B:ASP67
|
2.3
|
17.1
|
1.0
|
|
OE1
|
B:GLU11
|
2.3
|
15.9
|
1.0
|
|
OD2
|
B:ASP103
|
2.3
|
17.2
|
1.0
|
|
O
|
B:HOH533
|
2.4
|
6.6
|
1.0
|
|
O
|
B:HOH537
|
2.4
|
8.2
|
1.0
|
|
CG
|
B:ASP103
|
3.1
|
18.1
|
1.0
|
|
OD1
|
B:ASP103
|
3.2
|
17.3
|
1.0
|
|
CD
|
B:GLU11
|
3.3
|
15.1
|
1.0
|
|
CG
|
B:ASP67
|
3.3
|
16.6
|
1.0
|
|
CD
|
B:GLU69
|
3.5
|
17.5
|
1.0
|
|
OE2
|
B:GLU11
|
3.6
|
16.4
|
1.0
|
|
CA
|
B:CA302
|
3.9
|
12.9
|
1.0
|
|
OD2
|
B:ASP67
|
4.1
|
15.6
|
1.0
|
|
CA
|
B:ASP67
|
4.1
|
14.7
|
1.0
|
|
N
|
B:ARG68
|
4.2
|
14.5
|
1.0
|
|
CB
|
B:ASP67
|
4.2
|
15.4
|
1.0
|
|
OD1
|
B:ASN104
|
4.2
|
19.9
|
1.0
|
|
O
|
B:HOH253
|
4.3
|
10.2
|
1.0
|
|
N
|
B:GLU69
|
4.3
|
14.7
|
1.0
|
|
OD1
|
B:ASN12
|
4.3
|
23.9
|
1.0
|
|
OE2
|
B:GLU69
|
4.3
|
17.3
|
1.0
|
|
CG
|
B:GLU69
|
4.4
|
16.8
|
1.0
|
|
CB
|
B:GLU69
|
4.4
|
16.3
|
1.0
|
|
C
|
B:ASP67
|
4.4
|
15.3
|
1.0
|
|
O
|
B:HOH383
|
4.4
|
14.6
|
1.0
|
|
CB
|
B:ASP103
|
4.6
|
18.9
|
1.0
|
|
CG
|
B:GLU11
|
4.6
|
16.9
|
1.0
|
|
ND2
|
B:ASN12
|
4.6
|
22.2
|
1.0
|
|
O
|
B:HOH219
|
4.6
|
17.4
|
1.0
|
|
CB
|
A:PRO46
|
4.7
|
18.9
|
1.0
|
|
CG
|
B:ASN12
|
4.9
|
22.4
|
1.0
|
|
CB
|
B:GLU11
|
4.9
|
16.4
|
1.0
|
|
Calcium binding site 5 out
of 6 in 3qrb
Go back to
Calcium Binding Sites List in 3qrb
Calcium binding site 5 out
of 6 in the Crystal Structure of E-Cadherin EC1-2 P5A P6A
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 5 of Crystal Structure of E-Cadherin EC1-2 P5A P6A within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca302
b:12.9
occ:1.00
|
OD1
|
B:ASP100
|
2.2
|
17.1
|
1.0
|
|
OD1
|
B:ASP136
|
2.3
|
17.3
|
1.0
|
|
OE2
|
B:GLU11
|
2.3
|
16.4
|
1.0
|
|
OD1
|
B:ASP103
|
2.3
|
17.3
|
1.0
|
|
OE2
|
B:GLU69
|
2.4
|
17.3
|
1.0
|
|
O
|
B:GLN101
|
2.5
|
17.5
|
1.0
|
|
OE1
|
B:GLU69
|
2.7
|
17.7
|
1.0
|
|
CD
|
B:GLU69
|
2.9
|
17.5
|
1.0
|
|
CG
|
B:ASP100
|
3.3
|
17.1
|
1.0
|
|
CG
|
B:ASP136
|
3.4
|
17.2
|
1.0
|
|
CD
|
B:GLU11
|
3.4
|
15.1
|
1.0
|
|
CG
|
B:ASP103
|
3.4
|
18.1
|
1.0
|
|
C
|
B:GLN101
|
3.6
|
18.1
|
1.0
|
|
OE1
|
B:GLU11
|
3.8
|
15.9
|
1.0
|
|
N
|
B:GLN101
|
3.8
|
18.1
|
1.0
|
|
OD2
|
B:ASP100
|
3.9
|
16.9
|
1.0
|
|
CA
|
B:CA301
|
3.9
|
12.3
|
1.0
|
|
OD1
|
B:ASN104
|
4.0
|
19.9
|
1.0
|
|
CB
|
B:ASP136
|
4.0
|
16.1
|
1.0
|
|
OD2
|
B:ASP103
|
4.0
|
17.2
|
1.0
|
|
N
|
B:ASP103
|
4.1
|
18.0
|
1.0
|
|
CA
|
B:ASP136
|
4.2
|
16.2
|
1.0
|
|
CG
|
B:GLU69
|
4.3
|
16.8
|
1.0
|
|
OD2
|
B:ASP136
|
4.3
|
16.6
|
1.0
|
|
CA
|
B:GLN101
|
4.3
|
18.9
|
0.5
|
|
CA
|
B:GLN101
|
4.3
|
18.8
|
0.5
|
|
NE
|
B:ARG68
|
4.4
|
18.9
|
1.0
|
|
CB
|
B:ASP100
|
4.5
|
17.2
|
1.0
|
|
CA
|
B:ASP100
|
4.6
|
17.1
|
1.0
|
|
CB
|
B:ASP103
|
4.6
|
18.9
|
1.0
|
|
N
|
B:ASN102
|
4.7
|
18.6
|
1.0
|
|
C
|
B:ASP100
|
4.7
|
18.6
|
1.0
|
|
CG
|
B:GLU11
|
4.7
|
16.9
|
1.0
|
|
CA
|
B:ASP103
|
4.8
|
18.9
|
1.0
|
|
CA
|
B:ASN102
|
4.9
|
17.9
|
1.0
|
|
CB
|
B:GLN101
|
4.9
|
19.4
|
0.5
|
|
NH2
|
B:ARG68
|
4.9
|
17.5
|
1.0
|
|
CB
|
B:ARG68
|
4.9
|
14.9
|
1.0
|
|
C
|
B:ASN102
|
5.0
|
18.9
|
1.0
|
|
Calcium binding site 6 out
of 6 in 3qrb
Go back to
Calcium Binding Sites List in 3qrb
Calcium binding site 6 out
of 6 in the Crystal Structure of E-Cadherin EC1-2 P5A P6A
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 6 of Crystal Structure of E-Cadherin EC1-2 P5A P6A within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca303
b:15.8
occ:1.00
|
O
|
B:ASN104
|
2.3
|
19.9
|
1.0
|
|
O
|
B:ASN143
|
2.3
|
19.2
|
1.0
|
|
OD2
|
B:ASP195
|
2.3
|
19.4
|
1.0
|
|
OD1
|
B:ASN102
|
2.3
|
19.4
|
1.0
|
|
OD2
|
B:ASP136
|
2.4
|
16.6
|
1.0
|
|
OD2
|
B:ASP134
|
2.4
|
21.0
|
1.0
|
|
OD1
|
B:ASP134
|
2.6
|
19.1
|
1.0
|
|
CG
|
B:ASP134
|
2.8
|
20.8
|
1.0
|
|
CG
|
B:ASP195
|
3.3
|
21.6
|
1.0
|
|
CG
|
B:ASP136
|
3.4
|
17.2
|
1.0
|
|
C
|
B:ASN104
|
3.5
|
20.2
|
1.0
|
|
CG
|
B:ASN102
|
3.5
|
19.2
|
1.0
|
|
C
|
B:ASN143
|
3.5
|
18.2
|
1.0
|
|
CB
|
B:ASP195
|
3.8
|
19.7
|
1.0
|
|
CB
|
B:ASP136
|
3.8
|
16.1
|
1.0
|
|
ND2
|
B:ASN102
|
4.1
|
17.9
|
1.0
|
|
N
|
B:ASN104
|
4.2
|
18.2
|
1.0
|
|
CA
|
B:ASN104
|
4.3
|
19.5
|
1.0
|
|
OD1
|
B:ASP195
|
4.3
|
21.3
|
1.0
|
|
CB
|
B:ASP134
|
4.4
|
19.0
|
1.0
|
|
CA
|
B:ASN143
|
4.4
|
19.4
|
1.0
|
|
CB
|
B:ASN143
|
4.4
|
18.4
|
1.0
|
|
N
|
B:ALA144
|
4.5
|
18.9
|
1.0
|
|
CB
|
B:ASN104
|
4.5
|
18.4
|
1.0
|
|
N
|
B:ARG105
|
4.5
|
22.0
|
1.0
|
|
OD1
|
B:ASP136
|
4.6
|
17.3
|
1.0
|
|
CA
|
B:ALA144
|
4.6
|
19.2
|
1.0
|
|
CD1
|
B:LEU201
|
4.7
|
22.3
|
1.0
|
|
CA
|
B:ARG105
|
4.7
|
23.2
|
0.5
|
|
CB
|
B:ASN102
|
4.7
|
18.8
|
1.0
|
|
CA
|
B:ARG105
|
4.8
|
22.8
|
0.5
|
|
N
|
B:ASP136
|
4.8
|
15.4
|
1.0
|
|
CD
|
B:PRO106
|
4.8
|
22.5
|
1.0
|
|
C
|
B:ARG105
|
4.8
|
23.0
|
1.0
|
|
CA
|
B:ASN102
|
4.8
|
17.9
|
1.0
|
|
N
|
B:PRO106
|
4.9
|
22.6
|
1.0
|
|
CA
|
B:ASP136
|
5.0
|
16.2
|
1.0
|
|
C
|
B:ASN102
|
5.0
|
18.9
|
1.0
|
|
Reference:
J.Vendome,
S.Posy,
X.Jin,
F.Bahna,
G.Ahlsen,
L.Shapiro,
B.Honig.
Molecular Design Principles Underlying Beta-Strand Swapping in the Adhesive Dimerization of Cadherins. Nat.Struct.Mol.Biol. V. 18 693 2011.
ISSN: ISSN 1545-9993
PubMed: 21572446
DOI: 10.1038/NSMB.2051
Page generated: Sat Dec 12 04:27:15 2020
|
